MuscleExample is an R workspace containing the following objects:
tab: a matrix of 5000 rows and 15 columns
phenotype: a indicator vector which denotes which columns in
tab are arrays from normal (NORM) and inclusion body myositis
G: a list containing the source, title, and the
probe set IDs associated with 626 pathways
The full inflammatory myopathway dataset (which includes all probe sets and samples, including more NORM, IBM, and dermatomyositis arrays) and a more comprehensive pathway annotation list for the HG-U133A and other selected array platforms are available at http://www.chip.org/~ppark/PNAS05/
Although the objects contained in
MuscleExample are subsets of
the full dataset, the results obtained from running pathway analysis
MuscleExample are comparable to those obtained using the
full dataset. This example dataset contains 8 IBM and 7 NORM arrays.
The 5000 probe sets were selected by considering the variance of the
expression values of each probe set among the 15 arrays.
1 integer matrix, 1 numeric vector, and 1 list
Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S., Park P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the USA, 102, 13544-9.
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